Notice this is still a theory and not really a true fact.
What I believe is called the Split Timeline. That means whatever happened after Adult OoT and whatever happened when Link went back in time after laying the Master Sword to rest.
First we have OoT:
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OoT
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The above links above OoT are the Adult Timeline. The bottom ones are Child.
We have two games that happen nearly after OoT, but at the same time. Those are TWW and TP. And of course MM came before that.
........TWW-PH
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OOT
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MM...TP
So we have 4 games already pieced into this. That leaves, LOZ, AOL, ALTTP, LA, OOS, OOA, FS, FSA, and TMC.
We still have problems with TWW and the Master Sword being stuck under water. I am guessing that is where LOZ and AOL came, because back then the Master Sword was called the Magicial Sword. The Sword may have been released up from the seas, landed somewhere in AOL and Ganon was free once again.
.........TWW...PH...LOZ...AOL...
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OOT
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MM....TP
TMC, FS, and FSA do not really need to be placed together. However FS and FSA will be put together after PH and before ALTTP due to the fact that that both show similar geographies to ALTTP. Also, LA was a sequel to ALTTP, so we put it right after.
.........TWW...PH...LOZ...AOL...FS/FSA...ALTTP...LA
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OOT
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MM....TP
In OOS and OOA both TwinRovas were trying to revive Ganondorf. They used the sorrow and chaos to gather up energy to revive Ganon. And for what reason? To destroy the world. There was no Master Sword at this time and after ALTTP the Master Sword rested forever because it thought there was no more evil.
.........TWW...PH...LOZ...AOL...FS/FSA...ALTTP...LA...OOS/OOA
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OOT
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MM....TP
TMC basically can be placed anywhere on the timeline, but it should be placed somewhere way before FS and FSA due to the fact it explains the origins of Vaati.
.........TWW...PH...LOZ...AOL...FS/FSA...ALTTP...LA...OOS/OOA
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OOT
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MM....TP
--TMC???
I think that gives decent info and most people go with this theory, but I want to know what you think about it and possibly correct me of error.